The Shaibah facility in Iraq at which some of the abuse was alleged to have taken place. Photograph: al-Sweady inquiry/PA

This is not another Baha Mousa or another Abu Ghraib, the defence secretary, Michael Fallon told the Commons on Wednesday in response to the al-Sweady inquiry report into allegations of murder and mutiliation by British troops into Iraq.

He was referring to the death of a Basra hotel worker in British custody in 2003, and US troops’ abuse of prisoners at the notorious jail near Baghdad. It was an easy comparison for the defence secretary to make, and to reject.

Sir Thayne Forbes devoted most of the concluding passages in his 1,350-page report to damning criticism of the allegations that British troops had killed and tortured Iraqis at Camp Abu Naji after a fierce gunfight on 14 May 2004. The allegations which, to most independent observers, seemed scarcely credible from the start, were sustained by Iraqi witnesses until their lawyer, Phil Shiner, dropped them a year after the public inquiry began, and shortly before it ended.

Forbes’s report does, however, detail many examples of the ill-treatment of Iraqi detainees, including breaches of the Geneva conventions and a ban on techniques the governrment outlawed in 1972. In stark contrast to his attacks on the allegations of murder and mutiliaton inside Camp Abu Naji, Forbes uses moderate, even euphemistic, language to describe the numerous cases of abuse.

At one level, he says the behaviour was understandable, given that it occurred after one of the most violent clashes with Iraqi insurgents since the invasion of the country in 2003. British troops were completely unprepared for the hostile reception they received almost everywhere they went in southern Iraq. Some of the younger soldiers had never fired a shot in anger before.

Forbes says the armed ambush, which led to the Battle of Danny Boy, was “carried out by a large number of heavily armed Iraqi insurgents … bent on inflicting as much death, injury, and damage on British forces as they could”.

British troops were poorly trained, encouraging a pattern of abuse which has emerged in both Iraq and Afghanistan. The Iraq historic allegations team (IHAT) set up by the Ministry of Defence is investigating 55 fatalities and 197 cases of possible ill-treatment, mostly brought by Shiner’s firm, Public Interest Lawyers. Some of the cases have been sent to Sir George Newman, a former high court judge and chair of a separate Iraq judicial investigations body acting as a quasi-coroner’s court considering cases with no criminal charges attached.

The international criminal court (ICC) is conducting preliminary inquiries into allegations made by Public Interest Lawyers of British involvement in war crimes involving “systematic detainee abuse” in Iraq between 2003 until 2008.

According to the ICC report, the alleged crimes occurred in 14 military detention facilities and other locations under British forces’ control. “The alleged ill-treatment reportedly involved inter alia the following techniques: hooding of detainees; the use of sensory deprivation and isolation; sleep deprivation; food and water deprivation … mock executions and threats of rape, death, torture, indefinite detention and further violence … forced nakedness, sexual taunts.”

Some of these are described in Forbes’s report, which amounts to a snapshot of what British, US and probably other foreign forces were up to in Iraq.

In a separate but related move, the parliamentary intelligence and security committee said on Wednesday that because of further allegations it would off its inquiry into any MI5 and MI6 involvement in the abuse of detainees until after the general election.

Britain’s involvement in the rendition of terror suspects has been obscured by years of false denials. The truth behind allegations about the behaviour of British troops in Iraq has been similarly concealed by the MoD’s reluctance to be transparent.

Fallon told MPs that Shiner could have stopped the inquiry, sparing both soldiers’ distress and millions of pounds of taxpayers’ money. If the MoD had been more open in the first place, however, there would have been no need for Forbes’s public inquiry.